- modeller_usage - salilab.org

log files and processing multiple files
by abdullah ahmed 18 Mar '10

18 Mar '10

Dear Modeller users, I would like to ask for help on two problems: 1) I do not get log files after running optimization. I am certain that it is not a matter of them taking really long to be made because I have been using Modeller for 3 months now and I have not gotten a log file. I do however, get "pdb.ini" "pdb.rsr" and "pdb.D000001" (contains info on maximal shift, energy changes and gradients). 2) I have a series of molecules that I would like to apply the same constraints to, and then optimize. Is there a script I can use to optimize all the files in one go? Thanks in advance for the help, Abdullah _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969

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modeller and virtualenv
by Will Dampier 17 Mar '10

17 Mar '10

I've been trying to modeller to play nice with the virtualenv package management system. Has anyone had any success getting this to work? thanks Will

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Model refinement
by Ehab AlMoubarak 16 Mar '10

16 Mar '10

Dear All, I am modelling a potassium channel protein using a template with fairly low sequence similarity to my target, therefore, I am trying to put several restraints. I am struggling to deal with a long loop supposed to be extracellular: so its location to the rest of the protein is roughly known. As I am refining the model using MD, the loop location completely became wrong, I suppose that the absence of alignment in the refinement process is the reason (which covers only small area of the loop anyway). I don’t know if there is anyway to exclude the loop while refining the rest of the model, or to restraint the loop in an approximate location of the structure (like putting distance restraint) while refining it. I must say that the gap in alignment corresponds to the loop is well over 15 amino acids. Any thoughts are highly appreciated. My script is here: from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A'], self.residue_range('7:A', '30:A'),self.residue_range('107:A', '130:A')).only_atom_types('CA') #s2 = selection(self.chains['A'], self.residue_range('107:A', '130:A')).only_atom_types('CA') s2 = selection(self.chains['A'], self.residue_range('157:A', '180:A'),self.residue_range('217:A', '240:A')).only_atom_types('CA') #s4 = selection(self.chains['A'], self.residue_range('217:A', '240:A')).only_atom_types('CA') s5 = selection(self.chains['A']).only_atom_types('CA') s6 = selection(self.chains['B']).only_atom_types('CA') s7 = selection(self.chains['A'], self.residue_range('80:A', '135:A')).only_atom_types('CA') s8 = selection(self.chains['A'], self.residue_range('185:A', '250:A')).only_atom_types('CA') self.restraints.add(secondary_structure.alpha(self.residue_range('7:A', '30:A'))) #self.restraints.add(secondary_structure.alpha(self.residue_range('107:A', '130:A'))) self.restraints.add(secondary_structure.alpha(self.residue_range('157:A', '180:A'))) #self.restraints.add(secondary_structure.alpha(self.residue_range('217:A', '240:A'))) #self.restraints.add(secondary_structure.alpha(self.residue_range('73:A', '92:A'))) #self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) self.restraints.symmetry.append(symmetry(s7, s8, 1.0)) #self.restraints.symmetry.append(symmetry(s2, s3, 1.0)) #self.restraints.symmetry.append(symmetry(s3, s4, 1.0)) self.restraints.symmetry.append(symmetry(s5, s6, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) env = environ() # directories for input atom files env.schedule_scale = physical.values(default=1.0, soft_sphere=0.7) env.io.atom_files_directory = ['.', '../atom_files'] # Be sure to use 'MyModel' rather than 'automodel' here! a = MyModel(env, alnfile = 'task3Modified8.ali' , # alignment filename knowns = '1orq_9', # codes of the templates sequence = 'TASK3h27', # code of the target assess_methods=assess.DOPE) a.starting_model= 1 # index of the first model a.ending_model = 15 # index of the last model # Very thorough VTFM optimization: a.library_schedule = autosched.slow a.max_var_iterations = 300 # Thorough MD optimization: a.md_level = refine.slow # Repeat the whole cycle 2 times and do not stop unless obj.func. > 1E6 a.repeat_optimization = 2 a.max_molpdf = 1ttt a.make() # Get a list of all successfully built models from a.outputs ok_models = filter(lambda x: x['failure'] is None, a.outputs) # Rank the models by DOPE score key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) # Get top model m = ok_models[0] print "Top model: %s (DOPE score %.3f)" % (m['name'], m[key]) My best regards Ehab, Research student

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using the parallel job support
by Will Dampier 16 Mar '10

16 Mar '10

I'm trying to use the parallel job support built into modeller. I've gotten the jobs to work with "local_slave" workers but when I try to use ssh_slave workers I get an OSError "OSError [Errno 2] No such file or directory: '/opt/apps/Protein-Threading' from <ssh_clave on iblade003". I know that ssh_slaves require a shared memory space and I know that everything in properly mounted ... running: ssh iblade003 'ls /opt/apps/Protein-Threading' return the proper results. Any suggestions? Will

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automodel() known templates
by Rafik Ouerchefani 16 Mar '10

16 Mar '10

Hello, I'm following tutorials and the all-steps example. I would like to know if there is a function or a method to automate the selection of the templates to be used in automodel() as "knowns". In the examples, this selection is done manually from matrix.mat or compare.log files. Thanks - Rafik

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How should I fill in the missing rsidues with the same chain id, resnumber and HETATM keeping?
by wayj86 wayj86 16 Mar '10

16 Mar '10

Dear all, I am trying to fix a protein with 6 missing aa. This protein has a resid from 500 to 650, with three HETATM residues (N-glycan) from 800 to 802 ( discontinuous with the protein resnumber). Here is my script to run modeller: *First step: to build a model with blank chain ID and resnumber from 1 to 150:* # Homology modeling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['./', ':../atom_files'] # Read in HETATM records from template PDBs env.io.hetatm = True env.patch_default = False class MyModel(automodel): def select_atoms(self): # Select residues 41 and 46 (PDB numbering) return selection(self.residue_range('41', '46')) a = MyModel(env, alnfile = 'xy.pir', # alignment filename knowns = 'x', # sequence = 'y', assess_methods=(assess.DOPE, assess.GA341)) # code of the target a.starting_model= 1 # index of the first model a.ending_model = 10 # index of the last model # Very thorough VTFM optimization: a.library_schedule = autosched.slow a.max_var_iterations = 300 # Thorough MD optimization: a.md_level = refine.slow # Repeat the whole cycle 2 times and do not stop unless obj.func. > 1E6 a.repeat_optimization = 3 a.max_molpdf = 1e6 a.make() # Get a list of all successfully built models from a.outputs ok_models = filter(lambda x: x['failure'] is None, a.outputs) # Rank the models by DOPE score key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) # Get top model m = ok_models[0] print "Top model: %s (DOPE score %.3f)" % (m['name'], m[key]) By running this script I did got a model with missing residues fixed and HETATM keeping, but the chain ID was blank (because only one chain was built), and the resnumber was from 1 to 154. I did hope to keep the original chain ID and the resnum, so I try the rename_segments, like: *Second step: reassign the chain ID and resnumber:* # Example for: model.rename_segments() # This will assign new PDB single-character chain id's to all the chains # in the input PDB file (here there are two 'chains': protein and the HETATM # water molecules). from modeller import * # Read the MODEL with all HETATM and water records (so there are two 'chains'): env = environ() env.io.atom_files_directory = ['./', ':../atom_files'] env.io.hetatm = True mdl = model(env, file='y') # Assign new segment names and write out the new model: mdl.rename_segments(segment_ids='A', renumber_residues=[500, 650]) mdl.write(file='y.ini') Now in the final model y.ini the chain ID was defined as "A", and resnum was from 500 to 650. However, the HETATM residues was from 651 to 653, but not 800 to 802. So should I modify my scripts to fix the protein and keeping its original chain ID, resnumber and HETATM residues? Thank you very much for your attention. P.S. The HETATM residues are also in chain A, the same chain with the protein. -- Be the change you want to see in the world.

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Refine segments of a crystal structure
by Baptiste Legrand 16 Mar '10

16 Mar '10

Hi all, Is it possible to refine protein segments from a crystal structure using modeller as we can do for models (but in this case, without providing alignment and template files) ? Thanks. Best wishes, Baptiste

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alignment with modeller
by Knut J Bjuland 16 Mar '10

16 Mar '10

I used multiple alignment with protein sequence to get a better alignment with a template. Is this a good practice. What are the recommende settings in salign to get the best possible alignment.

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HETERODIMER GENERATION
by Ajeeta kaushiki 16 Mar '10

16 Mar '10

Hi I have to generate a hetero dimer . The entire length of protein is 1500 amino acid . The first dimer is from 150-410 aa and next one is from 786-1188 aa , I have modelled this two domains separately , Now I have to map it on a known Homo Dimer present in the template pdb to generate as a heterodimer . Kindly guide or is there any other way to merge the coordinates . Thanks & Regards Ajeeta

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question on mutate monomers script
by Andrew Voronkov 11 Mar '10

11 Mar '10

Dear Modeller users, I am trying to mutate several aminoacids in the PDB file. I ve used the scrtipt (mutate.py) attached for this, but I get the error given below. What can be the problem? As I understand I need only PDB file for this script execution. Do I need to write path to the libraries in the explicit way or it should get it from the environment setup? I haven't specified the full path. Sincerely yours, Andrew :~/Mutate> mod9v7 mutate.py 'import site' failed; use -v for traceback warning: Non-ASCII character '\xe2' in file mutate.py on line 11, but no encoding declared; see http://www.python.org/peps/pep-0263.html for details File "mutate.py", line 11 env.libs.topology.read(file=’$(LIB)/top_heav.lib’) ^ SyntaxError: invalid syntax edward@29:~/Mutate> Скачать присоединенный файл (mutate.py): # Example for: selection.mutate() # This will read a PDB file, change its sequence a little, build new # coordinates for any of the additional atoms using only the internal # geometry, and write the mutant PDB file. It can be seen as primitive, # but rapid comparative modeling for substitution mutants. For insertion # and deletion mutants, follow the standard comparative modeling procedure. from modeller import * env = environ() env.io.atom_files_directory = ['.', '../atom_files'] # Read the topology library with non-hydrogen atoms only: env.libs.topology.read(file=’$(LIB)/top_heav.lib’) # To produce a mutant with all hydrogens, uncomment this line: #env.libs.topology.read(file=’$(LIB)/top_allh.lib’) # Read the CHARMM parameter library: env.libs.parameters.read(file=’$(LIB)/par.lib’) # Read the original PDB file and copy its sequence to the alignment array: code = ’1ijy’ aln = alignment(env) mdl = model(env, file=code) aln.append_model(mdl, atom_files=code, align_codes=code) # Select the residues to be mutated: in this case all ASP residues: sel = selection(mdl).only_residue_types(’ASP’) # The second example is commented out; it selects residues ’1’ and ’10’. #sel = selection(mdl.residues[’1’], mdl.residues[’10’]) # Mutate the selected residues into HIS residues (neutral HIS): sel.mutate(residue_type=’ASN’) # Add the mutated sequence to the alignment arrays (it is now the second # sequence in the alignment): aln.append_model(mdl, align_codes=’1ijy-1’) # Generate molecular topology for the mutant: mdl.clear_topology() mdl.generate_topology(aln[’1ijy-1’]) # Transfer all the coordinates you can from the template native structure # to the mutant (this works even if the order of atoms in the native PDB # file is not standard): mdl.transfer_xyz(aln) # Build the remaining unknown coordinates for the mutant: mdl.build(initialize_xyz=False, build_method=’INTERNAL_COORDINATES’) # Write the mutant to a file: mdl.write(file=’1ijy-1.atm’)

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